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Student Blogging in
Clinical Bioinformatics
Mark Hoffman, Ph.D.
Asst. Dean Educational Innovation –
UMKC School of Medicine
Director UMKC Center for Health Insights
Assoc. Prof. Biomedical and Health Informatics,
Pediatrics (UMKC)
MEDB 5510 - Clinical Bioinformatics
• 500 level course in Department of Biomedical and
Health Informatics (DBHI)
– Students are Master’s candidates, MDs, Ph.D.
candidates
– No pre-reqs, some students have biology or clinical
backgrounds, other have technical (CS) backgrounds
• “Use informatics to learn biology, biology to learn
informatics”
• Require many assignments to be submitted by
blog
Blog Approach
• Each assignment provides textual and visual
deliverables
• Approx ½ of assignments were blog entries
– Worksheet and Word documents for others
• Allow students to select blog platform –
WordPress, BlogSpot or hosted
• No platform instruction provided
– Or requested by students
Blog Platform Selection
9
Blogspot:
8
• “Next Blog”
• Google integration
• Blog Archive by year, month
7
6
5
4
Wordpress:
3
2
• Wide variety of templates
• Less advertising
1
0
2014
2015
Wordpress
Blogspot
Example Assignment – Protein 3D
Structure
• Select a structure file for the protein encoded by your gene. Email
me with any hesitations about your choice.
• Using the sequence context approach, locate the site associated
with the variant from last week.
– If the site of the variant is not included in the structure, use OMIM and
identify another clinically relevant site.
– Document your decision process in your blog entry.
• Highlight the site of the variant and display screenshots with
multiple visuals, including at minimum:
– Space filling
– Ribbon
• Address these questions:
– Is the site of the variant surface exposed or interior?
– Do the protein structure prediction algorithms successfully predict the
type of site (alpha helix, sheet, turn) in which the amino acid is located
in the 3D structure?
Visual Communication
Writing – Creative Voice
Quote from student
• I made a post on my Facebook sharing my blog site. I
have many friends that are in the field of medical
research, nursing, doctors, and some that are still
college students, and I have received a lot of positive
feedback from them (mostly due to it being the BRCA1
gene) in the form of e-mail, text, and I talked about it
over supper with a few of my friends that had seen it.
One of my friends in college asked me if I would be
interested in speaking at a Pre-Med club/medical
fraternity chapter sometime about bioinformatics,
and how it has helped me along my path to become a
physician.
– Austin Althaber (with permission)
Using Blogs in Class
Positives
• Contemporary approach
• Develop visual and narrative
voice
• Encourage students to build
web presence and credibility
– Many viewed as a resource
they can point to in seeking
jobs
• Students take pride in their
entries and share them
• Students began reviewing
other student blogs to
improve their own
Challenges
• Occasional technical issues
• Attribution of visuals
• Free blogs link out to other
sites, no control over links
• Grading paradigm
– Rubric based
– Highlight but didn’t correct
grammar, English
– Visual talents vary widely